Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160515_230834_708
Start time	2016-05-15 23:08:34
Run time	16:27:45.497
Tasks executed	32
Tasks failed	1
Tasks failed names	idr2 rep1-rep2
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC9/ATAC9-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC9/ATAC9-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC10/ATAC10-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC10/ATAC10-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
System*	local
Cpus*	1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None	atac.bds.20160515_230834_708/task.postalign_bed.pool_tag_reps.line_405.id_28 atac.bds.20160515_230834_708/task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_29 atac.bds.20160515_230834_708/task.callpeak_macs2.macs2_atac_pooled.line_192.id_30 atac.bds.20160515_230834_708/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31 atac.bds.20160515_230834_708/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_32 atac.bds.20160515_230834_708/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33 atac.bds.20160515_230834_708/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_34 atac.bds.20160515_230834_708/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35 atac.bds.20160515_230834_708/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_36 atac.bds.20160515_230834_708/task.idr.idr2_rep1_rep2.line_61.id_37
thread_20	thread_Root	atac.bds.20160515_230834_708_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6 atac.bds.20160515_230834_708_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8 atac.bds.20160515_230834_708_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_9 atac.bds.20160515_230834_708_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_10 atac.bds.20160515_230834_708_parallel_20/task.postalign_bed.subsample_bedpe_rep1.line_116.id_11 atac.bds.20160515_230834_708_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_12 atac.bds.20160515_230834_708_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_13 atac.bds.20160515_230834_708_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_14 atac.bds.20160515_230834_708_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_15 atac.bds.20160515_230834_708_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_16 atac.bds.20160515_230834_708_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_17
thread_21	thread_Root	atac.bds.20160515_230834_708_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7 atac.bds.20160515_230834_708_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_18 atac.bds.20160515_230834_708_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_19 atac.bds.20160515_230834_708_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_20 atac.bds.20160515_230834_708_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_21 atac.bds.20160515_230834_708_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_22 atac.bds.20160515_230834_708_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_23 atac.bds.20160515_230834_708_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_24 atac.bds.20160515_230834_708_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_25 atac.bds.20160515_230834_708_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_26 atac.bds.20160515_230834_708_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_27

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6
Name	bowtie2_PE rep1
Thread	thread_20
PID	88361

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-05-15 23:08:36
End	2016-05-16 04:51:19
Elapsed	05:42:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.align.log
Dependencies

 
# SYS command. line 135

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 139

 bowtie2  -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.bam

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 39 files...

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7
Name	bowtie2_PE rep2
Thread	thread_21
PID	88366

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-05-15 23:08:36
End	2016-05-16 09:53:43
Elapsed	10:45:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.align.log
Dependencies

 
# SYS command. line 135

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 139

 bowtie2  -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.bam

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 79 files...

Num	3
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8
Name	dedup_bam_PE rep1
Thread	thread_20
PID	97349

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 04:51:20
End	2016-05-16 06:28:46
Elapsed	01:37:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
Dependencies

 
# SYS command. line 217

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 228

 echo

# SYS command. line 229

 samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark

# SYS command. line 230

 echo

# SYS command. line 237

 samtools fixmate -r /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 238

 samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 243

 export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"

# SYS command. line 244

 export MAX_JAVA_MEM="12G"

# SYS command. line 247

 if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
			java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			else \
			java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 265

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 267

 samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
			grep -v 'chrM' | sort | uniq -c | \
			awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1/m2}' > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam

   
--------------------Stdout--------------------



 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 23 files...
[bam_sort_core] merging from 23 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Mon May 16 05:42:36 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon May 16 05:42:36 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-16 05:42:36	MarkDuplicates	Start of doWork freeMemory: 254889840; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-16 05:42:36	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-16 05:42:36	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-16 05:42:42	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr10:128,004,598
INFO	2016-05-16 05:42:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:42:47	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    4s.  Last read position: chr11:107,713,464
INFO	2016-05-16 05:42:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 05:42:51	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    4s.  Last read position: chr12:99,101,091
INFO	2016-05-16 05:42:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:42:55	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    4s.  Last read position: chr14:23,499,403
INFO	2016-05-16 05:42:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 05:43:01	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    5s.  Last read position: chr15:63,648,805
INFO	2016-05-16 05:43:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 05:43:06	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    5s.  Last read position: chr16:73,776,412
INFO	2016-05-16 05:43:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:43:10	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    3s.  Last read position: chr17:75,051,408
INFO	2016-05-16 05:43:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:43:14	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    3s.  Last read position: chr19:30,017,055
INFO	2016-05-16 05:43:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 05:43:20	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    5s.  Last read position: chr1:36,897,460
INFO	2016-05-16 05:43:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:43:23	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    3s.  Last read position: chr1:181,224,755
INFO	2016-05-16 05:43:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 05:43:28	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    4s.  Last read position: chr20:48,402,858
INFO	2016-05-16 05:43:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 05:43:34	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    5s.  Last read position: chr2:16,341,525
INFO	2016-05-16 05:43:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 05:43:37	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    3s.  Last read position: chr2:154,152,526
INFO	2016-05-16 05:43:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:43:41	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    3s.  Last read position: chr3:38,760,092
INFO	2016-05-16 05:43:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:43:59	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:   17s.  Last read position: chr3:178,162,831
INFO	2016-05-16 05:43:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:44:02	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:26s.  Time for last 1,000,000:    3s.  Last read position: chr4:127,557,362
INFO	2016-05-16 05:44:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 05:44:06	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:30s.  Time for last 1,000,000:    3s.  Last read position: chr5:97,098,452
INFO	2016-05-16 05:44:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:44:10	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:    3s.  Last read position: chr6:16,217,184
INFO	2016-05-16 05:44:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:44:14	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    4s.  Last read position: chr6:159,419,780
INFO	2016-05-16 05:44:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:44:20	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:    5s.  Last read position: chr7:127,032,700
INFO	2016-05-16 05:44:20	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 05:44:24	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    3s.  Last read position: chr8:102,130,910
INFO	2016-05-16 05:44:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 05:44:27	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:51s.  Time for last 1,000,000:    3s.  Last read position: chr9:117,755,846
INFO	2016-05-16 05:44:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:44:31	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    3s.  Last read position: chrM:475
INFO	2016-05-16 05:44:31	MarkDuplicates	Tracking 9146 as yet unmatched pairs. 9146 records in RAM.
INFO	2016-05-16 05:44:34	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:911
INFO	2016-05-16 05:44:34	MarkDuplicates	Tracking 22912 as yet unmatched pairs. 22912 records in RAM.
INFO	2016-05-16 05:44:37	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,541
INFO	2016-05-16 05:44:37	MarkDuplicates	Tracking 28486 as yet unmatched pairs. 28486 records in RAM.
INFO	2016-05-16 05:44:43	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    6s.  Last read position: chrM:2,234
INFO	2016-05-16 05:44:43	MarkDuplicates	Tracking 20536 as yet unmatched pairs. 20536 records in RAM.
INFO	2016-05-16 05:44:46	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:10s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,727
INFO	2016-05-16 05:44:46	MarkDuplicates	Tracking 83304 as yet unmatched pairs. 83304 records in RAM.
INFO	2016-05-16 05:44:50	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,019
INFO	2016-05-16 05:44:50	MarkDuplicates	Tracking 48106 as yet unmatched pairs. 48106 records in RAM.
INFO	2016-05-16 05:44:55	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,335
INFO	2016-05-16 05:44:55	MarkDuplicates	Tracking 76624 as yet unmatched pairs. 76624 records in RAM.
INFO	2016-05-16 05:45:08	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:   12s.  Last read position: chrM:3,553
INFO	2016-05-16 05:45:08	MarkDuplicates	Tracking 3532 as yet unmatched pairs. 3532 records in RAM.
INFO	2016-05-16 05:45:11	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,769
INFO	2016-05-16 05:45:11	MarkDuplicates	Tracking 53064 as yet unmatched pairs. 53064 records in RAM.
INFO	2016-05-16 05:45:15	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,300
INFO	2016-05-16 05:45:15	MarkDuplicates	Tracking 14968 as yet unmatched pairs. 14968 records in RAM.
INFO	2016-05-16 05:45:19	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:42s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,311
INFO	2016-05-16 05:45:19	MarkDuplicates	Tracking 17522 as yet unmatched pairs. 17522 records in RAM.
INFO	2016-05-16 05:45:22	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:46s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,227
INFO	2016-05-16 05:45:22	MarkDuplicates	Tracking 32156 as yet unmatched pairs. 32156 records in RAM.
INFO	2016-05-16 05:45:26	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:02:50s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,472
INFO	2016-05-16 05:45:26	MarkDuplicates	Tracking 24088 as yet unmatched pairs. 24088 records in RAM.
INFO	2016-05-16 05:45:29	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,006
INFO	2016-05-16 05:45:29	MarkDuplicates	Tracking 14878 as yet unmatched pairs. 14878 records in RAM.
INFO	2016-05-16 05:45:32	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,862
INFO	2016-05-16 05:45:32	MarkDuplicates	Tracking 31530 as yet unmatched pairs. 31530 records in RAM.
INFO	2016-05-16 05:45:35	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:02:59s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,625
INFO	2016-05-16 05:45:35	MarkDuplicates	Tracking 5936 as yet unmatched pairs. 5936 records in RAM.
INFO	2016-05-16 05:45:38	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,401
INFO	2016-05-16 05:45:38	MarkDuplicates	Tracking 5168 as yet unmatched pairs. 5168 records in RAM.
INFO	2016-05-16 05:45:42	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,093
INFO	2016-05-16 05:45:42	MarkDuplicates	Tracking 31954 as yet unmatched pairs. 31954 records in RAM.
INFO	2016-05-16 05:45:45	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,652
INFO	2016-05-16 05:45:45	MarkDuplicates	Tracking 30780 as yet unmatched pairs. 30780 records in RAM.
INFO	2016-05-16 05:45:50	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,236
INFO	2016-05-16 05:45:50	MarkDuplicates	Tracking 36586 as yet unmatched pairs. 36586 records in RAM.
INFO	2016-05-16 05:45:53	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:17s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,771
INFO	2016-05-16 05:45:53	MarkDuplicates	Tracking 20536 as yet unmatched pairs. 20536 records in RAM.
INFO	2016-05-16 05:45:57	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,187
INFO	2016-05-16 05:45:57	MarkDuplicates	Tracking 23264 as yet unmatched pairs. 23264 records in RAM.
INFO	2016-05-16 05:46:04	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:28s.  Time for last 1,000,000:    7s.  Last read position: chrM:12,619
INFO	2016-05-16 05:46:04	MarkDuplicates	Tracking 52114 as yet unmatched pairs. 52114 records in RAM.
INFO	2016-05-16 05:46:07	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:31s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,089
INFO	2016-05-16 05:46:07	MarkDuplicates	Tracking 35568 as yet unmatched pairs. 35568 records in RAM.
INFO	2016-05-16 05:46:10	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:03:34s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,429
INFO	2016-05-16 05:46:10	MarkDuplicates	Tracking 34346 as yet unmatched pairs. 34346 records in RAM.
INFO	2016-05-16 05:46:13	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,917
INFO	2016-05-16 05:46:13	MarkDuplicates	Tracking 18834 as yet unmatched pairs. 18834 records in RAM.
INFO	2016-05-16 05:46:18	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    4s.  Last read position: chrM:14,419
INFO	2016-05-16 05:46:18	MarkDuplicates	Tracking 9978 as yet unmatched pairs. 9978 records in RAM.
INFO	2016-05-16 05:46:21	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,048
INFO	2016-05-16 05:46:21	MarkDuplicates	Tracking 93278 as yet unmatched pairs. 93278 records in RAM.
INFO	2016-05-16 05:46:25	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:03:48s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,279
INFO	2016-05-16 05:46:25	MarkDuplicates	Tracking 27942 as yet unmatched pairs. 27942 records in RAM.
INFO	2016-05-16 05:46:28	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,575
INFO	2016-05-16 05:46:28	MarkDuplicates	Tracking 21932 as yet unmatched pairs. 21932 records in RAM.
INFO	2016-05-16 05:46:31	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,821
INFO	2016-05-16 05:46:31	MarkDuplicates	Tracking 81784 as yet unmatched pairs. 81784 records in RAM.
INFO	2016-05-16 05:46:34	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:03:58s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,322
INFO	2016-05-16 05:46:34	MarkDuplicates	Tracking 49494 as yet unmatched pairs. 49494 records in RAM.
INFO	2016-05-16 05:46:37	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:01s.  Time for last 1,000,000:    3s.  Last read position: chrX:29,595,230
INFO	2016-05-16 05:46:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:46:40	MarkDuplicates	Read 55728728 records. 0 pairs never matched.
INFO	2016-05-16 05:46:48	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3083819776; totalMemory: 3110600704; maxMemory: 3817865216
INFO	2016-05-16 05:46:48	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-16 05:46:49	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-16 05:47:07	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-16 05:47:19	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-16 05:47:21	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2039484328; totalMemory: 3020423168; maxMemory: 3817865216
INFO	2016-05-16 05:47:21	MarkDuplicates	Marking 35262490 records as duplicates.
INFO	2016-05-16 05:47:21	MarkDuplicates	Found 10938300 optical duplicate clusters.
INFO	2016-05-16 05:48:58	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:36s.  Time for last 10,000,000:   96s.  Last read position: chr1:181,224,755
INFO	2016-05-16 05:50:34	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:12s.  Time for last 10,000,000:   95s.  Last read position: chr7:127,032,700
INFO	2016-05-16 05:51:56	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:34s.  Time for last 10,000,000:   82s.  Last read position: chrM:3,553
INFO	2016-05-16 05:53:12	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:50s.  Time for last 10,000,000:   75s.  Last read position: chrM:10,093
INFO	2016-05-16 05:54:35	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:13s.  Time for last 10,000,000:   83s.  Last read position: chrM:15,048
INFO	2016-05-16 05:55:22	MarkDuplicates	Before output close freeMemory: 3145157680; totalMemory: 3175088128; maxMemory: 3817865216
INFO	2016-05-16 05:55:22	MarkDuplicates	After output close freeMemory: 3145156560; totalMemory: 3175088128; maxMemory: 3817865216
[Mon May 16 05:55:22 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 12.77 minutes.
Runtime.totalMemory()=3175088128
[bam_sort_core] merging from 23 files...

Num	4
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_9
Name	nmsrt_bam rep1
Thread	thread_20
PID	99169

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 06:28:46
End	2016-05-16 06:38:37
Elapsed	00:09:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Dependencies

 
# SYS command. line 323

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 325

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.nmsrt

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 9 files...

Num	5
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_10
Name	bam_to_bedpe rep1
Thread	thread_20
PID	99395

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 06:38:37
End	2016-05-16 06:39:34
Elapsed	00:00:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Dependencies	nmsrt_bam rep1 nmsrt_bam rep1

 
# SYS command. line 427

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 430

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	6
ID	task.postalign_bed.subsample_bedpe_rep1.line_116.id_11
Name	subsample_bedpe rep1
Thread	thread_20
PID	99459

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 06:39:35
End	2016-05-16 06:40:25
Elapsed	00:00:49
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Dependencies

 
# SYS command. line 118

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 120

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	7
ID	task.postalign_bam.bedpe_to_tag_rep1.line_465.id_12
Name	bedpe_to_tag rep1
Thread	thread_20
PID	99525

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 06:40:26
End	2016-05-16 06:41:19
Elapsed	00:00:53
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Dependencies

 
# SYS command. line 467

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 469

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	8
ID	task.postalign_bed.shift_tag_rep1.line_140.id_13
Name	shift_tag rep1
Thread	thread_20
PID	99594

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 06:41:20
End	2016-05-16 06:42:12
Elapsed	00:00:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 144

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	9
ID	task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_14
Name	subsample_bedpe2tagrep1
Thread	thread_20
PID	99665

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 06:42:13
End	2016-05-16 06:42:36
Elapsed	00:00:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Dependencies

 
# SYS command. line 91

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 95

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | \
			grep -v "chrM" | shuf -n 25000000 | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	10
ID	task.postalign_bed.xcor_rep1.line_165.id_15
Name	xcor rep1
Thread	thread_20
PID	99728

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 06:42:36
End	2016-05-16 06:55:58
Elapsed	00:13:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
Dependencies

 
# SYS command. line 167

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 171

 Rscript $(which run_spp_nodups.R) -rf \
			-c=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc -speak=0

# SYS command. line 174

 sed -r 's/,[^\t]+//g' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 0 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpIk4uac/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign1863933b343ef
done. read 9408184 fragments
ChIP data read length 74 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1125057 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.13267687246943 
Top 3 estimates for fragment length 0 
Window half size 405 
Phantom peak location 65 
Phantom peak Correlation 0.1360169 
Normalized Strand cross-correlation coefficient (NSC) 1.17929 
Relative Strand Cross correlation Coefficient (RSC) 0.8579389 
Phantom Peak Quality Tag 0 
null device 
          1 

 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Loading required package: caTools

Num	11
ID	task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_16
Name	macs2_atac rep1.pval0.1
Thread	thread_20
PID	99733

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-05-16 06:42:36
End	2016-05-16 06:59:14
Elapsed	00:16:38
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 194

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 06:42:39: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 06:42:39: #1 read tag files... 
INFO  @ Mon, 16 May 2016 06:42:39: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 06:42:41:  1000000 
INFO  @ Mon, 16 May 2016 06:42:43:  2000000 
INFO  @ Mon, 16 May 2016 06:42:45:  3000000 
INFO  @ Mon, 16 May 2016 06:42:47:  4000000 
INFO  @ Mon, 16 May 2016 06:42:49:  5000000 
INFO  @ Mon, 16 May 2016 06:42:51:  6000000 
INFO  @ Mon, 16 May 2016 06:42:53:  7000000 
INFO  @ Mon, 16 May 2016 06:42:55:  8000000 
INFO  @ Mon, 16 May 2016 06:42:57:  9000000 
INFO  @ Mon, 16 May 2016 06:42:59:  10000000 
INFO  @ Mon, 16 May 2016 06:43:01:  11000000 
INFO  @ Mon, 16 May 2016 06:43:03:  12000000 
INFO  @ Mon, 16 May 2016 06:43:05:  13000000 
INFO  @ Mon, 16 May 2016 06:43:07:  14000000 
INFO  @ Mon, 16 May 2016 06:43:09:  15000000 
INFO  @ Mon, 16 May 2016 06:43:10:  16000000 
INFO  @ Mon, 16 May 2016 06:43:12:  17000000 
INFO  @ Mon, 16 May 2016 06:43:14:  18000000 
INFO  @ Mon, 16 May 2016 06:43:17: #1 tag size is determined as 51 bps 
INFO  @ Mon, 16 May 2016 06:43:17: #1 tag size = 51 
INFO  @ Mon, 16 May 2016 06:43:17: #1  total tags in treatment: 18816368 
INFO  @ Mon, 16 May 2016 06:43:17: #1 finished! 
INFO  @ Mon, 16 May 2016 06:43:17: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 06:43:17: #2 Skipped... 
INFO  @ Mon, 16 May 2016 06:43:17: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 06:43:17: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 06:43:17: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 06:43:17: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 06:43:17: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 06:43:57: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 06:46:05: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 06:46:11: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 06:46:14: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 06:46:18: Done! 
INFO  @ Mon, 16 May 2016 06:46:32: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 06:46:32: #1 read tag files... 
INFO  @ Mon, 16 May 2016 06:46:32: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 06:46:35:  1000000 
INFO  @ Mon, 16 May 2016 06:46:38:  2000000 
INFO  @ Mon, 16 May 2016 06:46:40:  3000000 
INFO  @ Mon, 16 May 2016 06:46:42:  4000000 
INFO  @ Mon, 16 May 2016 06:46:44:  5000000 
INFO  @ Mon, 16 May 2016 06:46:46:  6000000 
INFO  @ Mon, 16 May 2016 06:46:47:  7000000 
INFO  @ Mon, 16 May 2016 06:46:49:  8000000 
INFO  @ Mon, 16 May 2016 06:46:50:  9000000 
INFO  @ Mon, 16 May 2016 06:46:52:  10000000 
INFO  @ Mon, 16 May 2016 06:46:54:  11000000 
INFO  @ Mon, 16 May 2016 06:46:55:  12000000 
INFO  @ Mon, 16 May 2016 06:46:57:  13000000 
INFO  @ Mon, 16 May 2016 06:46:58:  14000000 
INFO  @ Mon, 16 May 2016 06:47:00:  15000000 
INFO  @ Mon, 16 May 2016 06:47:02:  16000000 
INFO  @ Mon, 16 May 2016 06:47:03:  17000000 
INFO  @ Mon, 16 May 2016 06:47:05:  18000000 
INFO  @ Mon, 16 May 2016 06:47:07: #1 tag size is determined as 51 bps 
INFO  @ Mon, 16 May 2016 06:47:07: #1 tag size = 51 
INFO  @ Mon, 16 May 2016 06:47:07: #1  total tags in treatment: 18816368 
INFO  @ Mon, 16 May 2016 06:47:07: #1 finished! 
INFO  @ Mon, 16 May 2016 06:47:07: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 06:47:07: #2 Skipped... 
INFO  @ Mon, 16 May 2016 06:47:07: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 06:47:07: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 06:47:07: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 06:47:07: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 06:47:07: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 06:47:07: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 06:47:43: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 06:47:43: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 06:47:43: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 06:47:43: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 06:47:43: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 06:58:41: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 06:58:52: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 06:59:00: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 06:59:05: Done!

Num	12
ID	task.callpeak_macs2.macs2_atac_rep1.line_192.id_17
Name	macs2_atac rep1
Thread	thread_20
PID	99746

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-05-16 06:42:37
End	2016-05-16 07:05:34
Elapsed	00:22:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
Dependencies

 
# SYS command. line 194

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_summits.bed

# SYS command. line 217

 if [[ true == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 06:42:39: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 06:42:39: #1 read tag files... 
INFO  @ Mon, 16 May 2016 06:42:39: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 06:42:41:  1000000 
INFO  @ Mon, 16 May 2016 06:42:43:  2000000 
INFO  @ Mon, 16 May 2016 06:42:45:  3000000 
INFO  @ Mon, 16 May 2016 06:42:47:  4000000 
INFO  @ Mon, 16 May 2016 06:42:49:  5000000 
INFO  @ Mon, 16 May 2016 06:42:51:  6000000 
INFO  @ Mon, 16 May 2016 06:42:53:  7000000 
INFO  @ Mon, 16 May 2016 06:42:54:  8000000 
INFO  @ Mon, 16 May 2016 06:42:56:  9000000 
INFO  @ Mon, 16 May 2016 06:42:59:  10000000 
INFO  @ Mon, 16 May 2016 06:43:00:  11000000 
INFO  @ Mon, 16 May 2016 06:43:02:  12000000 
INFO  @ Mon, 16 May 2016 06:43:04:  13000000 
INFO  @ Mon, 16 May 2016 06:43:06:  14000000 
INFO  @ Mon, 16 May 2016 06:43:08:  15000000 
INFO  @ Mon, 16 May 2016 06:43:10:  16000000 
INFO  @ Mon, 16 May 2016 06:43:12:  17000000 
INFO  @ Mon, 16 May 2016 06:43:14:  18000000 
INFO  @ Mon, 16 May 2016 06:43:17: #1 tag size is determined as 51 bps 
INFO  @ Mon, 16 May 2016 06:43:17: #1 tag size = 51 
INFO  @ Mon, 16 May 2016 06:43:17: #1  total tags in treatment: 18816368 
INFO  @ Mon, 16 May 2016 06:43:17: #1 finished! 
INFO  @ Mon, 16 May 2016 06:43:17: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 06:43:17: #2 Skipped... 
INFO  @ Mon, 16 May 2016 06:43:17: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 06:43:17: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 06:43:17: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 06:43:17: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 06:43:17: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 06:43:56: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 06:45:30: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 06:45:36: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 06:45:40: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 06:45:43: Done! 
INFO  @ Mon, 16 May 2016 06:45:58: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 06:45:58: #1 read tag files... 
INFO  @ Mon, 16 May 2016 06:45:58: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 06:46:00:  1000000 
INFO  @ Mon, 16 May 2016 06:46:02:  2000000 
INFO  @ Mon, 16 May 2016 06:46:03:  3000000 
INFO  @ Mon, 16 May 2016 06:46:05:  4000000 
INFO  @ Mon, 16 May 2016 06:46:07:  5000000 
INFO  @ Mon, 16 May 2016 06:46:09:  6000000 
INFO  @ Mon, 16 May 2016 06:46:10:  7000000 
INFO  @ Mon, 16 May 2016 06:46:12:  8000000 
INFO  @ Mon, 16 May 2016 06:46:14:  9000000 
INFO  @ Mon, 16 May 2016 06:46:15:  10000000 
INFO  @ Mon, 16 May 2016 06:46:17:  11000000 
INFO  @ Mon, 16 May 2016 06:46:19:  12000000 
INFO  @ Mon, 16 May 2016 06:46:20:  13000000 
INFO  @ Mon, 16 May 2016 06:46:22:  14000000 
INFO  @ Mon, 16 May 2016 06:46:23:  15000000 
INFO  @ Mon, 16 May 2016 06:46:25:  16000000 
INFO  @ Mon, 16 May 2016 06:46:27:  17000000 
INFO  @ Mon, 16 May 2016 06:46:28:  18000000 
INFO  @ Mon, 16 May 2016 06:46:31: #1 tag size is determined as 51 bps 
INFO  @ Mon, 16 May 2016 06:46:31: #1 tag size = 51 
INFO  @ Mon, 16 May 2016 06:46:31: #1  total tags in treatment: 18816368 
INFO  @ Mon, 16 May 2016 06:46:31: #1 finished! 
INFO  @ Mon, 16 May 2016 06:46:31: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 06:46:31: #2 Skipped... 
INFO  @ Mon, 16 May 2016 06:46:31: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 06:46:31: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 06:46:31: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 06:46:31: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 06:46:31: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 06:46:31: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 06:47:10: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 06:47:10: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 06:47:10: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 06:47:10: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 06:47:10: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 06:50:42: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 06:50:44: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 06:50:45: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Mon, 16 May 2016 06:50:46: Done! 
INFO  @ Mon, 16 May 2016 06:50:50: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 06:51:27: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 06:51:46: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 06:52:02: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 06:54:15: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 06:55:29: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 06:58:31: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 06:59:08: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 06:59:26: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 06:59:41: Values in your input bedGraph files will be multiplied by 18.816368 ... 
INFO  @ Mon, 16 May 2016 07:01:50: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 07:02:05: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 07:03:08: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

Num	13
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_18
Name	dedup_bam_PE rep2
Thread	thread_21
PID	103628

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 09:53:44
End	2016-05-16 13:18:50
Elapsed	03:25:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
Dependencies

 
# SYS command. line 217

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 228

 echo

# SYS command. line 229

 samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark

# SYS command. line 230

 echo

# SYS command. line 237

 samtools fixmate -r /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 238

 samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 243

 export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"

# SYS command. line 244

 export MAX_JAVA_MEM="12G"

# SYS command. line 247

 if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
			java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			else \
			java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 265

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 267

 samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
			grep -v 'chrM' | sort | uniq -c | \
			awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1/m2}' > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam

   
--------------------Stdout--------------------



 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 46 files...
[bam_sort_core] merging from 46 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Mon May 16 11:37:04 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon May 16 11:37:04 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-16 11:37:04	MarkDuplicates	Start of doWork freeMemory: 254889832; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-16 11:37:04	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-16 11:37:04	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-16 11:37:10	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    6s.  Last read position: chr10:72,319,294
INFO	2016-05-16 11:37:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:37:16	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    5s.  Last read position: chr10:125,579,807
INFO	2016-05-16 11:37:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:37:21	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    5s.  Last read position: chr11:45,743,014
INFO	2016-05-16 11:37:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:37:26	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:22s.  Time for last 1,000,000:    4s.  Last read position: chr11:103,975,525
INFO	2016-05-16 11:37:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:37:34	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    7s.  Last read position: chr12:23,057,129
INFO	2016-05-16 11:37:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:37:41	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    7s.  Last read position: chr12:90,357,714
INFO	2016-05-16 11:37:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:37:46	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    4s.  Last read position: chr13:31,102,261
INFO	2016-05-16 11:37:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:37:51	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    4s.  Last read position: chr13:104,210,461
INFO	2016-05-16 11:37:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:37:56	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    5s.  Last read position: chr14:73,565,939
INFO	2016-05-16 11:37:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:38:04	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    8s.  Last read position: chr15:46,551,348
INFO	2016-05-16 11:38:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:38:12	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:    7s.  Last read position: chr15:100,524,426
INFO	2016-05-16 11:38:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:38:16	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    4s.  Last read position: chr16:66,711,478
INFO	2016-05-16 11:38:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:38:22	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:17s.  Time for last 1,000,000:    5s.  Last read position: chr17:26,526,013
INFO	2016-05-16 11:38:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:38:26	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:    4s.  Last read position: chr17:74,976,604
INFO	2016-05-16 11:38:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:38:46	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:   19s.  Last read position: chr18:55,620,070
INFO	2016-05-16 11:38:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:38:51	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    5s.  Last read position: chr19:33,608,715
INFO	2016-05-16 11:38:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:38:56	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    4s.  Last read position: chr1:4,116,737
INFO	2016-05-16 11:38:56	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 11:39:02	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    5s.  Last read position: chr1:46,490,976
INFO	2016-05-16 11:39:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:39:06	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    4s.  Last read position: chr1:109,811,510
INFO	2016-05-16 11:39:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:39:10	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    4s.  Last read position: chr1:192,491,702
INFO	2016-05-16 11:39:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:39:15	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:    4s.  Last read position: chr1:248,569,105
INFO	2016-05-16 11:39:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:39:20	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    4s.  Last read position: chr20:54,360,873
INFO	2016-05-16 11:39:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:39:26	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    6s.  Last read position: chr22:30,273,924
INFO	2016-05-16 11:39:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:39:31	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:    4s.  Last read position: chr2:27,590,658
INFO	2016-05-16 11:39:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:39:35	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    3s.  Last read position: chr2:91,703,389
INFO	2016-05-16 11:39:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:39:41	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:37s.  Time for last 1,000,000:    6s.  Last read position: chr2:162,410,549
INFO	2016-05-16 11:39:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:39:45	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    3s.  Last read position: chr2:225,873,994
INFO	2016-05-16 11:39:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:39:49	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    3s.  Last read position: chr3:38,570,221
INFO	2016-05-16 11:39:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:39:53	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:49s.  Time for last 1,000,000:    4s.  Last read position: chr3:106,199,813
INFO	2016-05-16 11:39:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:40:05	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:   12s.  Last read position: chr3:169,856,976
INFO	2016-05-16 11:40:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:40:09	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    3s.  Last read position: chr4:29,901,313
INFO	2016-05-16 11:40:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:40:13	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    3s.  Last read position: chr4:107,891,152
INFO	2016-05-16 11:40:13	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 11:40:17	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:13s.  Time for last 1,000,000:    4s.  Last read position: chr4:181,298,258
INFO	2016-05-16 11:40:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:40:22	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:18s.  Time for last 1,000,000:    5s.  Last read position: chr5:63,661,351
INFO	2016-05-16 11:40:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:40:26	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    3s.  Last read position: chr5:133,647,309
INFO	2016-05-16 11:40:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:40:29	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    3s.  Last read position: chr5:172,181,872
INFO	2016-05-16 11:40:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:40:33	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:28s.  Time for last 1,000,000:    3s.  Last read position: chr6:42,421,022
INFO	2016-05-16 11:40:33	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-16 11:40:37	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    3s.  Last read position: chr6:116,619,586
INFO	2016-05-16 11:40:37	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 11:40:40	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:36s.  Time for last 1,000,000:    3s.  Last read position: chr7:5,466,360
INFO	2016-05-16 11:40:40	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-16 11:40:48	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:44s.  Time for last 1,000,000:    7s.  Last read position: chr7:77,025,097
INFO	2016-05-16 11:40:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:40:53	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:48s.  Time for last 1,000,000:    4s.  Last read position: chr7:139,979,740
INFO	2016-05-16 11:40:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:40:56	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    3s.  Last read position: chr8:41,707,447
INFO	2016-05-16 11:40:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:41:00	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    3s.  Last read position: chr8:111,693,131
INFO	2016-05-16 11:41:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:41:04	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    3s.  Last read position: chr9:27,788,952
INFO	2016-05-16 11:41:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:41:11	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    7s.  Last read position: chr9:120,709,280
INFO	2016-05-16 11:41:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:41:14	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:10s.  Time for last 1,000,000:    3s.  Last read position: chrM:113
INFO	2016-05-16 11:41:14	MarkDuplicates	Tracking 56020 as yet unmatched pairs. 56020 records in RAM.
INFO	2016-05-16 11:41:19	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:15s.  Time for last 1,000,000:    4s.  Last read position: chrM:468
INFO	2016-05-16 11:41:19	MarkDuplicates	Tracking 21228 as yet unmatched pairs. 21228 records in RAM.
INFO	2016-05-16 11:41:23	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:683
INFO	2016-05-16 11:41:23	MarkDuplicates	Tracking 65148 as yet unmatched pairs. 65148 records in RAM.
INFO	2016-05-16 11:41:26	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:22s.  Time for last 1,000,000:    3s.  Last read position: chrM:869
INFO	2016-05-16 11:41:26	MarkDuplicates	Tracking 56436 as yet unmatched pairs. 56436 records in RAM.
INFO	2016-05-16 11:41:30	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,292
INFO	2016-05-16 11:41:30	MarkDuplicates	Tracking 60896 as yet unmatched pairs. 60896 records in RAM.
INFO	2016-05-16 11:41:34	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,506
INFO	2016-05-16 11:41:34	MarkDuplicates	Tracking 73564 as yet unmatched pairs. 73564 records in RAM.
INFO	2016-05-16 11:41:38	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,833
INFO	2016-05-16 11:41:38	MarkDuplicates	Tracking 47920 as yet unmatched pairs. 47920 records in RAM.
INFO	2016-05-16 11:41:44	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:40s.  Time for last 1,000,000:    6s.  Last read position: chrM:2,167
INFO	2016-05-16 11:41:44	MarkDuplicates	Tracking 54546 as yet unmatched pairs. 54546 records in RAM.
INFO	2016-05-16 11:41:47	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,562
INFO	2016-05-16 11:41:47	MarkDuplicates	Tracking 60178 as yet unmatched pairs. 60178 records in RAM.
INFO	2016-05-16 11:41:51	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:46s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,709
INFO	2016-05-16 11:41:51	MarkDuplicates	Tracking 132600 as yet unmatched pairs. 132600 records in RAM.
INFO	2016-05-16 11:41:54	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,852
INFO	2016-05-16 11:41:54	MarkDuplicates	Tracking 184308 as yet unmatched pairs. 184308 records in RAM.
INFO	2016-05-16 11:41:57	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:53s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,016
INFO	2016-05-16 11:41:57	MarkDuplicates	Tracking 107256 as yet unmatched pairs. 107256 records in RAM.
INFO	2016-05-16 11:42:01	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:56s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,204
INFO	2016-05-16 11:42:01	MarkDuplicates	Tracking 137464 as yet unmatched pairs. 137464 records in RAM.
INFO	2016-05-16 11:42:18	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:   17s.  Last read position: chrM:3,334
INFO	2016-05-16 11:42:18	MarkDuplicates	Tracking 154712 as yet unmatched pairs. 154712 records in RAM.
INFO	2016-05-16 11:42:22	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:05:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,434
INFO	2016-05-16 11:42:22	MarkDuplicates	Tracking 115654 as yet unmatched pairs. 115654 records in RAM.
INFO	2016-05-16 11:42:26	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:05:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,578
INFO	2016-05-16 11:42:26	MarkDuplicates	Tracking 33100 as yet unmatched pairs. 33100 records in RAM.
INFO	2016-05-16 11:42:29	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:05:25s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,688
INFO	2016-05-16 11:42:29	MarkDuplicates	Tracking 137678 as yet unmatched pairs. 137678 records in RAM.
INFO	2016-05-16 11:42:33	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,810
INFO	2016-05-16 11:42:33	MarkDuplicates	Tracking 129436 as yet unmatched pairs. 129436 records in RAM.
INFO	2016-05-16 11:42:37	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:05:33s.  Time for last 1,000,000:    4s.  Last read position: chrM:4,013
INFO	2016-05-16 11:42:37	MarkDuplicates	Tracking 31286 as yet unmatched pairs. 31286 records in RAM.
INFO	2016-05-16 11:42:41	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,698
INFO	2016-05-16 11:42:41	MarkDuplicates	Tracking 12436 as yet unmatched pairs. 12436 records in RAM.
INFO	2016-05-16 11:42:44	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:05:40s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,970
INFO	2016-05-16 11:42:44	MarkDuplicates	Tracking 73120 as yet unmatched pairs. 73120 records in RAM.
INFO	2016-05-16 11:42:50	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:46s.  Time for last 1,000,000:    5s.  Last read position: chrM:5,357
INFO	2016-05-16 11:42:50	MarkDuplicates	Tracking 56642 as yet unmatched pairs. 56642 records in RAM.
INFO	2016-05-16 11:42:53	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,994
INFO	2016-05-16 11:42:53	MarkDuplicates	Tracking 33428 as yet unmatched pairs. 33428 records in RAM.
INFO	2016-05-16 11:42:57	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:05:52s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,256
INFO	2016-05-16 11:42:57	MarkDuplicates	Tracking 66760 as yet unmatched pairs. 66760 records in RAM.
INFO	2016-05-16 11:43:00	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:05:55s.  Time for last 1,000,000:    2s.  Last read position: chrM:6,414
INFO	2016-05-16 11:43:00	MarkDuplicates	Tracking 55924 as yet unmatched pairs. 55924 records in RAM.
INFO	2016-05-16 11:43:03	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:05:58s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,546
INFO	2016-05-16 11:43:03	MarkDuplicates	Tracking 55240 as yet unmatched pairs. 55240 records in RAM.
INFO	2016-05-16 11:43:06	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:06:01s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,913
INFO	2016-05-16 11:43:06	MarkDuplicates	Tracking 81308 as yet unmatched pairs. 81308 records in RAM.
INFO	2016-05-16 11:43:09	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:06:05s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,224
INFO	2016-05-16 11:43:09	MarkDuplicates	Tracking 34696 as yet unmatched pairs. 34696 records in RAM.
INFO	2016-05-16 11:43:17	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    7s.  Last read position: chrM:7,794
INFO	2016-05-16 11:43:17	MarkDuplicates	Tracking 28824 as yet unmatched pairs. 28824 records in RAM.
INFO	2016-05-16 11:43:21	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    4s.  Last read position: chrM:8,002
INFO	2016-05-16 11:43:21	MarkDuplicates	Tracking 49930 as yet unmatched pairs. 49930 records in RAM.
INFO	2016-05-16 11:43:24	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:06:20s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,404
INFO	2016-05-16 11:43:24	MarkDuplicates	Tracking 24682 as yet unmatched pairs. 24682 records in RAM.
INFO	2016-05-16 11:43:28	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,929
INFO	2016-05-16 11:43:28	MarkDuplicates	Tracking 20154 as yet unmatched pairs. 20154 records in RAM.
INFO	2016-05-16 11:43:31	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:06:26s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,268
INFO	2016-05-16 11:43:31	MarkDuplicates	Tracking 43146 as yet unmatched pairs. 43146 records in RAM.
INFO	2016-05-16 11:43:34	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:    2s.  Last read position: chrM:9,619
INFO	2016-05-16 11:43:34	MarkDuplicates	Tracking 32900 as yet unmatched pairs. 32900 records in RAM.
INFO	2016-05-16 11:43:37	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:06:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,874
INFO	2016-05-16 11:43:37	MarkDuplicates	Tracking 109046 as yet unmatched pairs. 109046 records in RAM.
INFO	2016-05-16 11:43:41	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:06:36s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,169
INFO	2016-05-16 11:43:41	MarkDuplicates	Tracking 51130 as yet unmatched pairs. 51130 records in RAM.
INFO	2016-05-16 11:43:44	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:06:40s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,407
INFO	2016-05-16 11:43:44	MarkDuplicates	Tracking 79384 as yet unmatched pairs. 79384 records in RAM.
INFO	2016-05-16 11:43:48	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:06:43s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,660
INFO	2016-05-16 11:43:48	MarkDuplicates	Tracking 45668 as yet unmatched pairs. 45668 records in RAM.
INFO	2016-05-16 11:43:54	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:06:50s.  Time for last 1,000,000:    6s.  Last read position: chrM:11,138
INFO	2016-05-16 11:43:54	MarkDuplicates	Tracking 60534 as yet unmatched pairs. 60534 records in RAM.
INFO	2016-05-16 11:43:57	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,305
INFO	2016-05-16 11:43:57	MarkDuplicates	Tracking 46364 as yet unmatched pairs. 46364 records in RAM.
INFO	2016-05-16 11:44:01	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:06:56s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,543
INFO	2016-05-16 11:44:01	MarkDuplicates	Tracking 90836 as yet unmatched pairs. 90836 records in RAM.
INFO	2016-05-16 11:44:05	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:07:00s.  Time for last 1,000,000:    4s.  Last read position: chrM:11,829
INFO	2016-05-16 11:44:05	MarkDuplicates	Tracking 19306 as yet unmatched pairs. 19306 records in RAM.
INFO	2016-05-16 11:44:09	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:07:05s.  Time for last 1,000,000:    4s.  Last read position: chrM:12,066
INFO	2016-05-16 11:44:09	MarkDuplicates	Tracking 34962 as yet unmatched pairs. 34962 records in RAM.
INFO	2016-05-16 11:44:25	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:   16s.  Last read position: chrM:12,351
INFO	2016-05-16 11:44:25	MarkDuplicates	Tracking 43520 as yet unmatched pairs. 43520 records in RAM.
INFO	2016-05-16 11:44:29	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:07:25s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,547
INFO	2016-05-16 11:44:29	MarkDuplicates	Tracking 83988 as yet unmatched pairs. 83988 records in RAM.
INFO	2016-05-16 11:44:34	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:07:29s.  Time for last 1,000,000:    4s.  Last read position: chrM:12,680
INFO	2016-05-16 11:44:34	MarkDuplicates	Tracking 124124 as yet unmatched pairs. 124124 records in RAM.
INFO	2016-05-16 11:44:37	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:07:33s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,985
INFO	2016-05-16 11:44:37	MarkDuplicates	Tracking 15576 as yet unmatched pairs. 15576 records in RAM.
INFO	2016-05-16 11:44:41	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:07:37s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,161
INFO	2016-05-16 11:44:41	MarkDuplicates	Tracking 57878 as yet unmatched pairs. 57878 records in RAM.
INFO	2016-05-16 11:44:47	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:07:42s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,334
INFO	2016-05-16 11:44:47	MarkDuplicates	Tracking 64850 as yet unmatched pairs. 64850 records in RAM.
INFO	2016-05-16 11:44:51	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:07:46s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,506
INFO	2016-05-16 11:44:51	MarkDuplicates	Tracking 53046 as yet unmatched pairs. 53046 records in RAM.
INFO	2016-05-16 11:44:54	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:07:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,769
INFO	2016-05-16 11:44:54	MarkDuplicates	Tracking 26514 as yet unmatched pairs. 26514 records in RAM.
INFO	2016-05-16 11:44:59	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:07:54s.  Time for last 1,000,000:    4s.  Last read position: chrM:13,953
INFO	2016-05-16 11:44:59	MarkDuplicates	Tracking 55162 as yet unmatched pairs. 55162 records in RAM.
INFO	2016-05-16 11:45:03	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:07:59s.  Time for last 1,000,000:    4s.  Last read position: chrM:14,270
INFO	2016-05-16 11:45:03	MarkDuplicates	Tracking 43710 as yet unmatched pairs. 43710 records in RAM.
INFO	2016-05-16 11:45:07	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:08:03s.  Time for last 1,000,000:    4s.  Last read position: chrM:14,465
INFO	2016-05-16 11:45:07	MarkDuplicates	Tracking 37396 as yet unmatched pairs. 37396 records in RAM.
INFO	2016-05-16 11:45:12	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:08:07s.  Time for last 1,000,000:    4s.  Last read position: chrM:14,916
INFO	2016-05-16 11:45:12	MarkDuplicates	Tracking 62252 as yet unmatched pairs. 62252 records in RAM.
INFO	2016-05-16 11:45:16	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:08:12s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,067
INFO	2016-05-16 11:45:16	MarkDuplicates	Tracking 164752 as yet unmatched pairs. 164752 records in RAM.
INFO	2016-05-16 11:45:20	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:08:16s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,192
INFO	2016-05-16 11:45:20	MarkDuplicates	Tracking 50078 as yet unmatched pairs. 50078 records in RAM.
INFO	2016-05-16 11:45:29	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:08:25s.  Time for last 1,000,000:    8s.  Last read position: chrM:15,337
INFO	2016-05-16 11:45:29	MarkDuplicates	Tracking 93888 as yet unmatched pairs. 93888 records in RAM.
INFO	2016-05-16 11:45:35	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:08:31s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,466
INFO	2016-05-16 11:45:35	MarkDuplicates	Tracking 35498 as yet unmatched pairs. 35498 records in RAM.
INFO	2016-05-16 11:45:39	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:08:34s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,603
INFO	2016-05-16 11:45:39	MarkDuplicates	Tracking 51536 as yet unmatched pairs. 51536 records in RAM.
INFO	2016-05-16 11:45:42	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:08:38s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,729
INFO	2016-05-16 11:45:42	MarkDuplicates	Tracking 100152 as yet unmatched pairs. 100152 records in RAM.
INFO	2016-05-16 11:45:46	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:08:41s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,839
INFO	2016-05-16 11:45:46	MarkDuplicates	Tracking 137504 as yet unmatched pairs. 137504 records in RAM.
INFO	2016-05-16 11:45:49	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:08:45s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,059
INFO	2016-05-16 11:45:49	MarkDuplicates	Tracking 64102 as yet unmatched pairs. 64102 records in RAM.
INFO	2016-05-16 11:45:52	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:08:48s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,328
INFO	2016-05-16 11:45:52	MarkDuplicates	Tracking 97556 as yet unmatched pairs. 97556 records in RAM.
INFO	2016-05-16 11:45:56	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:08:51s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,438
INFO	2016-05-16 11:45:56	MarkDuplicates	Tracking 58590 as yet unmatched pairs. 58590 records in RAM.
INFO	2016-05-16 11:45:59	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:08:55s.  Time for last 1,000,000:    3s.  Last read position: chrX:34,826,939
INFO	2016-05-16 11:45:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:46:03	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:08:59s.  Time for last 1,000,000:    4s.  Last read position: chrX:120,451,384
INFO	2016-05-16 11:46:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:46:06	MarkDuplicates	Read 112486288 records. 0 pairs never matched.
INFO	2016-05-16 11:46:15	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2995287528; totalMemory: 3022520320; maxMemory: 3817865216
INFO	2016-05-16 11:46:15	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-16 11:46:15	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-16 11:47:03	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-16 11:47:30	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-16 11:47:35	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2052191088; totalMemory: 3034054656; maxMemory: 3817865216
INFO	2016-05-16 11:47:35	MarkDuplicates	Marking 75201558 records as duplicates.
INFO	2016-05-16 11:47:35	MarkDuplicates	Found 24625117 optical duplicate clusters.
INFO	2016-05-16 11:49:20	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:44s.  Time for last 10,000,000:  104s.  Last read position: chr15:46,551,348
INFO	2016-05-16 11:51:02	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:25s.  Time for last 10,000,000:  101s.  Last read position: chr1:192,491,702
INFO	2016-05-16 11:52:43	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:06s.  Time for last 10,000,000:  101s.  Last read position: chr3:169,856,976
INFO	2016-05-16 11:54:41	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:07:04s.  Time for last 10,000,000:  118s.  Last read position: chr7:77,025,097
INFO	2016-05-16 11:56:21	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:45s.  Time for last 10,000,000:  100s.  Last read position: chrM:1,292
INFO	2016-05-16 11:58:00	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:10:24s.  Time for last 10,000,000:   98s.  Last read position: chrM:3,434
INFO	2016-05-16 11:59:36	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:11:59s.  Time for last 10,000,000:   95s.  Last read position: chrM:6,414
INFO	2016-05-16 12:01:04	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:13:27s.  Time for last 10,000,000:   87s.  Last read position: chrM:9,874
INFO	2016-05-16 12:02:26	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:14:49s.  Time for last 10,000,000:   82s.  Last read position: chrM:12,547
INFO	2016-05-16 12:03:45	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:16:09s.  Time for last 10,000,000:   79s.  Last read position: chrM:14,916
INFO	2016-05-16 12:05:06	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:17:30s.  Time for last 10,000,000:   80s.  Last read position: chrM:16,438
INFO	2016-05-16 12:05:32	MarkDuplicates	Before output close freeMemory: 3139882152; totalMemory: 3170369536; maxMemory: 3817865216
INFO	2016-05-16 12:05:32	MarkDuplicates	After output close freeMemory: 3139881096; totalMemory: 3170369536; maxMemory: 3817865216
[Mon May 16 12:05:32 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 28.47 minutes.
Runtime.totalMemory()=3170369536
[bam_sort_core] merging from 46 files...

Num	14
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_19
Name	nmsrt_bam rep2
Thread	thread_21
PID	111420

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 13:18:50
End	2016-05-16 13:34:04
Elapsed	00:15:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Dependencies

 
# SYS command. line 323

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 325

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.nmsrt

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 16 files...

Num	15
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_20
Name	bam_to_bedpe rep2
Thread	thread_21
PID	112612

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 13:34:04
End	2016-05-16 13:35:50
Elapsed	00:01:46
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Dependencies	nmsrt_bam rep2 nmsrt_bam rep2

 
# SYS command. line 427

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 430

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	16
ID	task.postalign_bed.subsample_bedpe_rep2.line_116.id_21
Name	subsample_bedpe rep2
Thread	thread_21
PID	112681

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 13:35:51
End	2016-05-16 13:37:52
Elapsed	00:02:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Dependencies

 
# SYS command. line 118

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 120

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	17
ID	task.postalign_bam.bedpe_to_tag_rep2.line_465.id_22
Name	bedpe_to_tag rep2
Thread	thread_21
PID	112811

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 13:37:53
End	2016-05-16 13:39:30
Elapsed	00:01:37
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Dependencies

 
# SYS command. line 467

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 469

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	18
ID	task.postalign_bed.shift_tag_rep2.line_140.id_23
Name	shift_tag rep2
Thread	thread_21
PID	112896

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 13:39:31
End	2016-05-16 13:40:37
Elapsed	00:01:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 144

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	19
ID	task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_24
Name	subsample_bedpe2tagrep2
Thread	thread_21
PID	112959

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 13:40:38
End	2016-05-16 13:41:45
Elapsed	00:01:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Dependencies

 
# SYS command. line 91

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 95

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | \
			grep -v "chrM" | shuf -n 25000000 | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	20
ID	task.postalign_bed.xcor_rep2.line_165.id_25
Name	xcor rep2
Thread	thread_21
PID	113026

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 13:41:45
End	2016-05-16 14:11:26
Elapsed	00:29:41
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
Dependencies

 
# SYS command. line 167

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 171

 Rscript $(which run_spp_nodups.R) -rf \
			-c=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc -speak=0

# SYS command. line 174

 sed -r 's/,[^\t]+//g' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 0 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpFYOWSJ/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign1ba2b571aeff4
done. read 17555158 fragments
ChIP data read length 75 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1863544 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.207718656323949 
Top 3 estimates for fragment length 0 
Window half size 440 
Phantom peak location 65 
Phantom peak Correlation 0.2106116 
Normalized Strand cross-correlation coefficient (NSC) 1.114643 
Relative Strand Cross correlation Coefficient (RSC) 0.8807394 
Phantom Peak Quality Tag 0 
null device 
          1 

 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Loading required package: caTools

Num	21
ID	task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_26
Name	macs2_atac rep2.pval0.1
Thread	thread_21
PID	113028

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-05-16 13:41:46
End	2016-05-16 14:00:42
Elapsed	00:18:56
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 194

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 13:41:50: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 13:41:50: #1 read tag files... 
INFO  @ Mon, 16 May 2016 13:41:50: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 13:41:52:  1000000 
INFO  @ Mon, 16 May 2016 13:41:54:  2000000 
INFO  @ Mon, 16 May 2016 13:41:55:  3000000 
INFO  @ Mon, 16 May 2016 13:41:57:  4000000 
INFO  @ Mon, 16 May 2016 13:41:59:  5000000 
INFO  @ Mon, 16 May 2016 13:42:01:  6000000 
INFO  @ Mon, 16 May 2016 13:42:03:  7000000 
INFO  @ Mon, 16 May 2016 13:42:04:  8000000 
INFO  @ Mon, 16 May 2016 13:42:06:  9000000 
INFO  @ Mon, 16 May 2016 13:42:08:  10000000 
INFO  @ Mon, 16 May 2016 13:42:09:  11000000 
INFO  @ Mon, 16 May 2016 13:42:11:  12000000 
INFO  @ Mon, 16 May 2016 13:42:13:  13000000 
INFO  @ Mon, 16 May 2016 13:42:15:  14000000 
INFO  @ Mon, 16 May 2016 13:42:16:  15000000 
INFO  @ Mon, 16 May 2016 13:42:18:  16000000 
INFO  @ Mon, 16 May 2016 13:42:20:  17000000 
INFO  @ Mon, 16 May 2016 13:42:22:  18000000 
INFO  @ Mon, 16 May 2016 13:42:23:  19000000 
INFO  @ Mon, 16 May 2016 13:42:25:  20000000 
INFO  @ Mon, 16 May 2016 13:42:27:  21000000 
INFO  @ Mon, 16 May 2016 13:42:29:  22000000 
INFO  @ Mon, 16 May 2016 13:42:30:  23000000 
INFO  @ Mon, 16 May 2016 13:42:32:  24000000 
INFO  @ Mon, 16 May 2016 13:42:34:  25000000 
INFO  @ Mon, 16 May 2016 13:42:36:  26000000 
INFO  @ Mon, 16 May 2016 13:42:37:  27000000 
INFO  @ Mon, 16 May 2016 13:42:39:  28000000 
INFO  @ Mon, 16 May 2016 13:42:41:  29000000 
INFO  @ Mon, 16 May 2016 13:42:42:  30000000 
INFO  @ Mon, 16 May 2016 13:42:44:  31000000 
INFO  @ Mon, 16 May 2016 13:42:46:  32000000 
INFO  @ Mon, 16 May 2016 13:42:47:  33000000 
INFO  @ Mon, 16 May 2016 13:42:49:  34000000 
INFO  @ Mon, 16 May 2016 13:42:51:  35000000 
INFO  @ Mon, 16 May 2016 13:42:53: #1 tag size is determined as 58 bps 
INFO  @ Mon, 16 May 2016 13:42:53: #1 tag size = 58 
INFO  @ Mon, 16 May 2016 13:42:53: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 13:42:53: #1 finished! 
INFO  @ Mon, 16 May 2016 13:42:53: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 13:42:53: #2 Skipped... 
INFO  @ Mon, 16 May 2016 13:42:53: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 13:42:53: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 13:42:53: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 13:42:53: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 13:42:53: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 13:44:21: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 13:47:02: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 13:47:06: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 13:47:09: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 13:47:12: Done! 
INFO  @ Mon, 16 May 2016 13:47:30: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 13:47:30: #1 read tag files... 
INFO  @ Mon, 16 May 2016 13:47:30: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 13:47:32:  1000000 
INFO  @ Mon, 16 May 2016 13:47:34:  2000000 
INFO  @ Mon, 16 May 2016 13:47:37:  3000000 
INFO  @ Mon, 16 May 2016 13:47:38:  4000000 
INFO  @ Mon, 16 May 2016 13:47:40:  5000000 
INFO  @ Mon, 16 May 2016 13:47:42:  6000000 
INFO  @ Mon, 16 May 2016 13:47:43:  7000000 
INFO  @ Mon, 16 May 2016 13:47:45:  8000000 
INFO  @ Mon, 16 May 2016 13:47:46:  9000000 
INFO  @ Mon, 16 May 2016 13:47:48:  10000000 
INFO  @ Mon, 16 May 2016 13:47:50:  11000000 
INFO  @ Mon, 16 May 2016 13:47:51:  12000000 
INFO  @ Mon, 16 May 2016 13:47:53:  13000000 
INFO  @ Mon, 16 May 2016 13:47:55:  14000000 
INFO  @ Mon, 16 May 2016 13:47:57:  15000000 
INFO  @ Mon, 16 May 2016 13:47:59:  16000000 
INFO  @ Mon, 16 May 2016 13:48:01:  17000000 
INFO  @ Mon, 16 May 2016 13:48:02:  18000000 
INFO  @ Mon, 16 May 2016 13:48:04:  19000000 
INFO  @ Mon, 16 May 2016 13:48:06:  20000000 
INFO  @ Mon, 16 May 2016 13:48:07:  21000000 
INFO  @ Mon, 16 May 2016 13:48:09:  22000000 
INFO  @ Mon, 16 May 2016 13:48:11:  23000000 
INFO  @ Mon, 16 May 2016 13:48:13:  24000000 
INFO  @ Mon, 16 May 2016 13:48:16:  25000000 
INFO  @ Mon, 16 May 2016 13:48:18:  26000000 
INFO  @ Mon, 16 May 2016 13:48:20:  27000000 
INFO  @ Mon, 16 May 2016 13:48:21:  28000000 
INFO  @ Mon, 16 May 2016 13:48:23:  29000000 
INFO  @ Mon, 16 May 2016 13:48:25:  30000000 
INFO  @ Mon, 16 May 2016 13:48:27:  31000000 
INFO  @ Mon, 16 May 2016 13:48:29:  32000000 
INFO  @ Mon, 16 May 2016 13:48:30:  33000000 
INFO  @ Mon, 16 May 2016 13:48:32:  34000000 
INFO  @ Mon, 16 May 2016 13:48:34:  35000000 
INFO  @ Mon, 16 May 2016 13:48:37: #1 tag size is determined as 58 bps 
INFO  @ Mon, 16 May 2016 13:48:37: #1 tag size = 58 
INFO  @ Mon, 16 May 2016 13:48:37: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 13:48:37: #1 finished! 
INFO  @ Mon, 16 May 2016 13:48:37: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 13:48:37: #2 Skipped... 
INFO  @ Mon, 16 May 2016 13:48:37: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 13:48:37: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 13:48:37: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 13:48:37: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 13:48:37: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 13:48:37: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 13:50:21: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 13:50:21: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 13:50:21: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 13:50:21: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 13:50:21: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 14:00:20: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 14:00:29: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 14:00:33: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 14:00:36: Done!

Num	22
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_27
Name	macs2_atac rep2
Thread	thread_21
PID	113039

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-05-16 13:41:46
End	2016-05-16 14:26:40
Elapsed	00:44:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
Dependencies

 
# SYS command. line 194

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_summits.bed

# SYS command. line 217

 if [[ true == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 13:41:50: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 13:41:50: #1 read tag files... 
INFO  @ Mon, 16 May 2016 13:41:50: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 13:41:52:  1000000 
INFO  @ Mon, 16 May 2016 13:41:53:  2000000 
INFO  @ Mon, 16 May 2016 13:41:55:  3000000 
INFO  @ Mon, 16 May 2016 13:41:57:  4000000 
INFO  @ Mon, 16 May 2016 13:41:59:  5000000 
INFO  @ Mon, 16 May 2016 13:42:01:  6000000 
INFO  @ Mon, 16 May 2016 13:42:02:  7000000 
INFO  @ Mon, 16 May 2016 13:42:04:  8000000 
INFO  @ Mon, 16 May 2016 13:42:06:  9000000 
INFO  @ Mon, 16 May 2016 13:42:08:  10000000 
INFO  @ Mon, 16 May 2016 13:42:10:  11000000 
INFO  @ Mon, 16 May 2016 13:42:12:  12000000 
INFO  @ Mon, 16 May 2016 13:42:14:  13000000 
INFO  @ Mon, 16 May 2016 13:42:16:  14000000 
INFO  @ Mon, 16 May 2016 13:42:18:  15000000 
INFO  @ Mon, 16 May 2016 13:42:19:  16000000 
INFO  @ Mon, 16 May 2016 13:42:21:  17000000 
INFO  @ Mon, 16 May 2016 13:42:23:  18000000 
INFO  @ Mon, 16 May 2016 13:42:25:  19000000 
INFO  @ Mon, 16 May 2016 13:42:27:  20000000 
INFO  @ Mon, 16 May 2016 13:42:28:  21000000 
INFO  @ Mon, 16 May 2016 13:42:30:  22000000 
INFO  @ Mon, 16 May 2016 13:42:32:  23000000 
INFO  @ Mon, 16 May 2016 13:42:34:  24000000 
INFO  @ Mon, 16 May 2016 13:42:36:  25000000 
INFO  @ Mon, 16 May 2016 13:42:37:  26000000 
INFO  @ Mon, 16 May 2016 13:42:39:  27000000 
INFO  @ Mon, 16 May 2016 13:42:41:  28000000 
INFO  @ Mon, 16 May 2016 13:42:43:  29000000 
INFO  @ Mon, 16 May 2016 13:42:44:  30000000 
INFO  @ Mon, 16 May 2016 13:42:46:  31000000 
INFO  @ Mon, 16 May 2016 13:42:48:  32000000 
INFO  @ Mon, 16 May 2016 13:42:50:  33000000 
INFO  @ Mon, 16 May 2016 13:42:51:  34000000 
INFO  @ Mon, 16 May 2016 13:42:53:  35000000 
INFO  @ Mon, 16 May 2016 13:42:56: #1 tag size is determined as 58 bps 
INFO  @ Mon, 16 May 2016 13:42:56: #1 tag size = 58 
INFO  @ Mon, 16 May 2016 13:42:56: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 13:42:56: #1 finished! 
INFO  @ Mon, 16 May 2016 13:42:56: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 13:42:56: #2 Skipped... 
INFO  @ Mon, 16 May 2016 13:42:56: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 13:42:56: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 13:42:56: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 13:42:56: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 13:42:56: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 13:44:21: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 13:46:27: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 13:46:31: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 13:46:34: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 13:46:36: Done! 
INFO  @ Mon, 16 May 2016 13:46:55: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 13:46:55: #1 read tag files... 
INFO  @ Mon, 16 May 2016 13:46:55: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 13:46:57:  1000000 
INFO  @ Mon, 16 May 2016 13:46:59:  2000000 
INFO  @ Mon, 16 May 2016 13:47:00:  3000000 
INFO  @ Mon, 16 May 2016 13:47:02:  4000000 
INFO  @ Mon, 16 May 2016 13:47:04:  5000000 
INFO  @ Mon, 16 May 2016 13:47:05:  6000000 
INFO  @ Mon, 16 May 2016 13:47:07:  7000000 
INFO  @ Mon, 16 May 2016 13:47:09:  8000000 
INFO  @ Mon, 16 May 2016 13:47:11:  9000000 
INFO  @ Mon, 16 May 2016 13:47:12:  10000000 
INFO  @ Mon, 16 May 2016 13:47:15:  11000000 
INFO  @ Mon, 16 May 2016 13:47:17:  12000000 
INFO  @ Mon, 16 May 2016 13:47:19:  13000000 
INFO  @ Mon, 16 May 2016 13:47:20:  14000000 
INFO  @ Mon, 16 May 2016 13:47:22:  15000000 
INFO  @ Mon, 16 May 2016 13:47:24:  16000000 
INFO  @ Mon, 16 May 2016 13:47:26:  17000000 
INFO  @ Mon, 16 May 2016 13:47:28:  18000000 
INFO  @ Mon, 16 May 2016 13:47:30:  19000000 
INFO  @ Mon, 16 May 2016 13:47:31:  20000000 
INFO  @ Mon, 16 May 2016 13:47:33:  21000000 
INFO  @ Mon, 16 May 2016 13:47:35:  22000000 
INFO  @ Mon, 16 May 2016 13:47:36:  23000000 
INFO  @ Mon, 16 May 2016 13:47:38:  24000000 
INFO  @ Mon, 16 May 2016 13:47:39:  25000000 
INFO  @ Mon, 16 May 2016 13:47:41:  26000000 
INFO  @ Mon, 16 May 2016 13:47:43:  27000000 
INFO  @ Mon, 16 May 2016 13:47:44:  28000000 
INFO  @ Mon, 16 May 2016 13:47:46:  29000000 
INFO  @ Mon, 16 May 2016 13:47:48:  30000000 
INFO  @ Mon, 16 May 2016 13:47:49:  31000000 
INFO  @ Mon, 16 May 2016 13:47:51:  32000000 
INFO  @ Mon, 16 May 2016 13:47:52:  33000000 
INFO  @ Mon, 16 May 2016 13:47:54:  34000000 
INFO  @ Mon, 16 May 2016 13:47:56:  35000000 
INFO  @ Mon, 16 May 2016 13:47:58: #1 tag size is determined as 58 bps 
INFO  @ Mon, 16 May 2016 13:47:58: #1 tag size = 58 
INFO  @ Mon, 16 May 2016 13:47:58: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 13:47:58: #1 finished! 
INFO  @ Mon, 16 May 2016 13:47:58: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 13:47:58: #2 Skipped... 
INFO  @ Mon, 16 May 2016 13:47:58: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 13:47:58: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 13:47:58: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 13:47:58: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 13:47:58: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 13:47:58: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 13:49:35: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 13:49:35: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 13:49:35: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 13:49:35: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 13:49:35: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 13:54:47: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 13:54:49: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 13:54:51: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Mon, 16 May 2016 13:54:51: Done! 
INFO  @ Mon, 16 May 2016 13:54:54: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 13:56:11: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 13:56:46: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 13:57:13: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 14:00:59: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 14:03:25: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 14:10:40: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 14:11:59: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 14:12:36: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 14:13:07: Values in your input bedGraph files will be multiplied by 35.000000 ... 
INFO  @ Mon, 16 May 2016 14:16:59: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 14:17:36: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 14:19:52: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

Num	23
ID	task.postalign_bed.pool_tag_reps.line_405.id_28
Name	pool_tag reps
Thread	thread_Root
PID	116670

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 14:26:41
End	2016-05-16 14:27:57
Elapsed	00:01:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Dependencies

 
# SYS command. line 407

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 408

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz  | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	24
ID	task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_29
Name	macs2_atac pooled.pval0.1
Thread	thread_Root
PID	116989

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-05-16 14:27:58
End	2016-05-16 14:51:58
Elapsed	00:24:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 194

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 14:28:00: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 14:28:00: #1 read tag files... 
INFO  @ Mon, 16 May 2016 14:28:00: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 14:28:02:  1000000 
INFO  @ Mon, 16 May 2016 14:28:04:  2000000 
INFO  @ Mon, 16 May 2016 14:28:06:  3000000 
INFO  @ Mon, 16 May 2016 14:28:08:  4000000 
INFO  @ Mon, 16 May 2016 14:28:09:  5000000 
INFO  @ Mon, 16 May 2016 14:28:11:  6000000 
INFO  @ Mon, 16 May 2016 14:28:13:  7000000 
INFO  @ Mon, 16 May 2016 14:28:14:  8000000 
INFO  @ Mon, 16 May 2016 14:28:16:  9000000 
INFO  @ Mon, 16 May 2016 14:28:18:  10000000 
INFO  @ Mon, 16 May 2016 14:28:19:  11000000 
INFO  @ Mon, 16 May 2016 14:28:21:  12000000 
INFO  @ Mon, 16 May 2016 14:28:23:  13000000 
INFO  @ Mon, 16 May 2016 14:28:24:  14000000 
INFO  @ Mon, 16 May 2016 14:28:26:  15000000 
INFO  @ Mon, 16 May 2016 14:28:28:  16000000 
INFO  @ Mon, 16 May 2016 14:28:30:  17000000 
INFO  @ Mon, 16 May 2016 14:28:31:  18000000 
INFO  @ Mon, 16 May 2016 14:28:33:  19000000 
INFO  @ Mon, 16 May 2016 14:28:35:  20000000 
INFO  @ Mon, 16 May 2016 14:28:36:  21000000 
INFO  @ Mon, 16 May 2016 14:28:38:  22000000 
INFO  @ Mon, 16 May 2016 14:28:40:  23000000 
INFO  @ Mon, 16 May 2016 14:28:41:  24000000 
INFO  @ Mon, 16 May 2016 14:28:43:  25000000 
INFO  @ Mon, 16 May 2016 14:28:45:  26000000 
INFO  @ Mon, 16 May 2016 14:28:46:  27000000 
INFO  @ Mon, 16 May 2016 14:28:48:  28000000 
INFO  @ Mon, 16 May 2016 14:28:50:  29000000 
INFO  @ Mon, 16 May 2016 14:28:51:  30000000 
INFO  @ Mon, 16 May 2016 14:28:53:  31000000 
INFO  @ Mon, 16 May 2016 14:28:54:  32000000 
INFO  @ Mon, 16 May 2016 14:28:56:  33000000 
INFO  @ Mon, 16 May 2016 14:28:58:  34000000 
INFO  @ Mon, 16 May 2016 14:28:59:  35000000 
INFO  @ Mon, 16 May 2016 14:29:01:  36000000 
INFO  @ Mon, 16 May 2016 14:29:03:  37000000 
INFO  @ Mon, 16 May 2016 14:29:04:  38000000 
INFO  @ Mon, 16 May 2016 14:29:06:  39000000 
INFO  @ Mon, 16 May 2016 14:29:07:  40000000 
INFO  @ Mon, 16 May 2016 14:29:09:  41000000 
INFO  @ Mon, 16 May 2016 14:29:11:  42000000 
INFO  @ Mon, 16 May 2016 14:29:12:  43000000 
INFO  @ Mon, 16 May 2016 14:29:14:  44000000 
INFO  @ Mon, 16 May 2016 14:29:15:  45000000 
INFO  @ Mon, 16 May 2016 14:29:17:  46000000 
INFO  @ Mon, 16 May 2016 14:29:19:  47000000 
INFO  @ Mon, 16 May 2016 14:29:20:  48000000 
INFO  @ Mon, 16 May 2016 14:29:22:  49000000 
INFO  @ Mon, 16 May 2016 14:29:23:  50000000 
INFO  @ Mon, 16 May 2016 14:29:25:  51000000 
INFO  @ Mon, 16 May 2016 14:29:27:  52000000 
INFO  @ Mon, 16 May 2016 14:29:28:  53000000 
INFO  @ Mon, 16 May 2016 14:29:34: #1 tag size is determined as 51 bps 
INFO  @ Mon, 16 May 2016 14:29:34: #1 tag size = 51 
INFO  @ Mon, 16 May 2016 14:29:34: #1  total tags in treatment: 53816368 
INFO  @ Mon, 16 May 2016 14:29:34: #1 finished! 
INFO  @ Mon, 16 May 2016 14:29:34: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 14:29:34: #2 Skipped... 
INFO  @ Mon, 16 May 2016 14:29:34: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 14:29:34: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 14:29:34: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 14:29:34: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 14:29:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 14:31:31: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 14:35:06: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 14:35:10: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 14:35:12: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 14:35:14: Done! 
INFO  @ Mon, 16 May 2016 14:35:26: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 14:35:26: #1 read tag files... 
INFO  @ Mon, 16 May 2016 14:35:26: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 14:35:28:  1000000 
INFO  @ Mon, 16 May 2016 14:35:29:  2000000 
INFO  @ Mon, 16 May 2016 14:35:31:  3000000 
INFO  @ Mon, 16 May 2016 14:35:32:  4000000 
INFO  @ Mon, 16 May 2016 14:35:34:  5000000 
INFO  @ Mon, 16 May 2016 14:35:36:  6000000 
INFO  @ Mon, 16 May 2016 14:35:37:  7000000 
INFO  @ Mon, 16 May 2016 14:35:39:  8000000 
INFO  @ Mon, 16 May 2016 14:35:40:  9000000 
INFO  @ Mon, 16 May 2016 14:35:42:  10000000 
INFO  @ Mon, 16 May 2016 14:35:44:  11000000 
INFO  @ Mon, 16 May 2016 14:35:45:  12000000 
INFO  @ Mon, 16 May 2016 14:35:47:  13000000 
INFO  @ Mon, 16 May 2016 14:35:49:  14000000 
INFO  @ Mon, 16 May 2016 14:35:50:  15000000 
INFO  @ Mon, 16 May 2016 14:35:52:  16000000 
INFO  @ Mon, 16 May 2016 14:35:54:  17000000 
INFO  @ Mon, 16 May 2016 14:35:56:  18000000 
INFO  @ Mon, 16 May 2016 14:35:57:  19000000 
INFO  @ Mon, 16 May 2016 14:35:59:  20000000 
INFO  @ Mon, 16 May 2016 14:36:01:  21000000 
INFO  @ Mon, 16 May 2016 14:36:02:  22000000 
INFO  @ Mon, 16 May 2016 14:36:04:  23000000 
INFO  @ Mon, 16 May 2016 14:36:05:  24000000 
INFO  @ Mon, 16 May 2016 14:36:07:  25000000 
INFO  @ Mon, 16 May 2016 14:36:09:  26000000 
INFO  @ Mon, 16 May 2016 14:36:10:  27000000 
INFO  @ Mon, 16 May 2016 14:36:12:  28000000 
INFO  @ Mon, 16 May 2016 14:36:14:  29000000 
INFO  @ Mon, 16 May 2016 14:36:15:  30000000 
INFO  @ Mon, 16 May 2016 14:36:17:  31000000 
INFO  @ Mon, 16 May 2016 14:36:19:  32000000 
INFO  @ Mon, 16 May 2016 14:36:20:  33000000 
INFO  @ Mon, 16 May 2016 14:36:22:  34000000 
INFO  @ Mon, 16 May 2016 14:36:24:  35000000 
INFO  @ Mon, 16 May 2016 14:36:25:  36000000 
INFO  @ Mon, 16 May 2016 14:36:27:  37000000 
INFO  @ Mon, 16 May 2016 14:36:29:  38000000 
INFO  @ Mon, 16 May 2016 14:36:30:  39000000 
INFO  @ Mon, 16 May 2016 14:36:32:  40000000 
INFO  @ Mon, 16 May 2016 14:36:34:  41000000 
INFO  @ Mon, 16 May 2016 14:36:35:  42000000 
INFO  @ Mon, 16 May 2016 14:36:37:  43000000 
INFO  @ Mon, 16 May 2016 14:36:39:  44000000 
INFO  @ Mon, 16 May 2016 14:36:40:  45000000 
INFO  @ Mon, 16 May 2016 14:36:42:  46000000 
INFO  @ Mon, 16 May 2016 14:36:43:  47000000 
INFO  @ Mon, 16 May 2016 14:36:45:  48000000 
INFO  @ Mon, 16 May 2016 14:36:47:  49000000 
INFO  @ Mon, 16 May 2016 14:36:49:  50000000 
INFO  @ Mon, 16 May 2016 14:36:51:  51000000 
INFO  @ Mon, 16 May 2016 14:36:52:  52000000 
INFO  @ Mon, 16 May 2016 14:36:54:  53000000 
INFO  @ Mon, 16 May 2016 14:36:59: #1 tag size is determined as 51 bps 
INFO  @ Mon, 16 May 2016 14:36:59: #1 tag size = 51 
INFO  @ Mon, 16 May 2016 14:36:59: #1  total tags in treatment: 53816368 
INFO  @ Mon, 16 May 2016 14:36:59: #1 finished! 
INFO  @ Mon, 16 May 2016 14:36:59: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 14:36:59: #2 Skipped... 
INFO  @ Mon, 16 May 2016 14:36:59: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 14:36:59: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 14:36:59: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 14:36:59: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 14:36:59: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 14:36:59: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 14:39:22: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 14:39:22: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 14:39:22: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 14:39:22: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 14:39:22: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 14:51:33: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 14:51:40: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 14:51:46: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 14:51:49: Done!

Num	25
ID	task.callpeak_macs2.macs2_atac_pooled.line_192.id_30
Name	macs2_atac pooled
Thread	thread_Root
PID	116991

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-05-16 14:27:58
End	2016-05-16 15:36:01
Elapsed	01:08:03
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig
Dependencies

 
# SYS command. line 194

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_summits.bed

# SYS command. line 217

 if [[ true == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 14:28:00: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 14:28:00: #1 read tag files... 
INFO  @ Mon, 16 May 2016 14:28:00: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 14:28:02:  1000000 
INFO  @ Mon, 16 May 2016 14:28:04:  2000000 
INFO  @ Mon, 16 May 2016 14:28:06:  3000000 
INFO  @ Mon, 16 May 2016 14:28:07:  4000000 
INFO  @ Mon, 16 May 2016 14:28:09:  5000000 
INFO  @ Mon, 16 May 2016 14:28:10:  6000000 
INFO  @ Mon, 16 May 2016 14:28:12:  7000000 
INFO  @ Mon, 16 May 2016 14:28:14:  8000000 
INFO  @ Mon, 16 May 2016 14:28:16:  9000000 
INFO  @ Mon, 16 May 2016 14:28:18:  10000000 
INFO  @ Mon, 16 May 2016 14:28:20:  11000000 
INFO  @ Mon, 16 May 2016 14:28:21:  12000000 
INFO  @ Mon, 16 May 2016 14:28:23:  13000000 
INFO  @ Mon, 16 May 2016 14:28:25:  14000000 
INFO  @ Mon, 16 May 2016 14:28:26:  15000000 
INFO  @ Mon, 16 May 2016 14:28:28:  16000000 
INFO  @ Mon, 16 May 2016 14:28:30:  17000000 
INFO  @ Mon, 16 May 2016 14:28:32:  18000000 
INFO  @ Mon, 16 May 2016 14:28:33:  19000000 
INFO  @ Mon, 16 May 2016 14:28:35:  20000000 
INFO  @ Mon, 16 May 2016 14:28:37:  21000000 
INFO  @ Mon, 16 May 2016 14:28:39:  22000000 
INFO  @ Mon, 16 May 2016 14:28:40:  23000000 
INFO  @ Mon, 16 May 2016 14:28:42:  24000000 
INFO  @ Mon, 16 May 2016 14:28:43:  25000000 
INFO  @ Mon, 16 May 2016 14:28:45:  26000000 
INFO  @ Mon, 16 May 2016 14:28:47:  27000000 
INFO  @ Mon, 16 May 2016 14:28:48:  28000000 
INFO  @ Mon, 16 May 2016 14:28:50:  29000000 
INFO  @ Mon, 16 May 2016 14:28:53:  30000000 
INFO  @ Mon, 16 May 2016 14:28:54:  31000000 
INFO  @ Mon, 16 May 2016 14:28:56:  32000000 
INFO  @ Mon, 16 May 2016 14:28:58:  33000000 
INFO  @ Mon, 16 May 2016 14:29:00:  34000000 
INFO  @ Mon, 16 May 2016 14:29:01:  35000000 
INFO  @ Mon, 16 May 2016 14:29:03:  36000000 
INFO  @ Mon, 16 May 2016 14:29:05:  37000000 
INFO  @ Mon, 16 May 2016 14:29:06:  38000000 
INFO  @ Mon, 16 May 2016 14:29:08:  39000000 
INFO  @ Mon, 16 May 2016 14:29:10:  40000000 
INFO  @ Mon, 16 May 2016 14:29:11:  41000000 
INFO  @ Mon, 16 May 2016 14:29:13:  42000000 
INFO  @ Mon, 16 May 2016 14:29:14:  43000000 
INFO  @ Mon, 16 May 2016 14:29:16:  44000000 
INFO  @ Mon, 16 May 2016 14:29:18:  45000000 
INFO  @ Mon, 16 May 2016 14:29:20:  46000000 
INFO  @ Mon, 16 May 2016 14:29:21:  47000000 
INFO  @ Mon, 16 May 2016 14:29:23:  48000000 
INFO  @ Mon, 16 May 2016 14:29:25:  49000000 
INFO  @ Mon, 16 May 2016 14:29:27:  50000000 
INFO  @ Mon, 16 May 2016 14:29:28:  51000000 
INFO  @ Mon, 16 May 2016 14:29:30:  52000000 
INFO  @ Mon, 16 May 2016 14:29:32:  53000000 
INFO  @ Mon, 16 May 2016 14:29:37: #1 tag size is determined as 51 bps 
INFO  @ Mon, 16 May 2016 14:29:37: #1 tag size = 51 
INFO  @ Mon, 16 May 2016 14:29:37: #1  total tags in treatment: 53816368 
INFO  @ Mon, 16 May 2016 14:29:37: #1 finished! 
INFO  @ Mon, 16 May 2016 14:29:37: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 14:29:37: #2 Skipped... 
INFO  @ Mon, 16 May 2016 14:29:37: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 14:29:37: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 14:29:37: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 14:29:37: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 14:29:37: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 14:31:48: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 14:34:36: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 14:34:39: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 14:34:41: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 14:34:44: Done! 
INFO  @ Mon, 16 May 2016 14:34:56: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 14:34:56: #1 read tag files... 
INFO  @ Mon, 16 May 2016 14:34:56: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 14:34:57:  1000000 
INFO  @ Mon, 16 May 2016 14:34:59:  2000000 
INFO  @ Mon, 16 May 2016 14:35:01:  3000000 
INFO  @ Mon, 16 May 2016 14:35:02:  4000000 
INFO  @ Mon, 16 May 2016 14:35:04:  5000000 
INFO  @ Mon, 16 May 2016 14:35:06:  6000000 
INFO  @ Mon, 16 May 2016 14:35:07:  7000000 
INFO  @ Mon, 16 May 2016 14:35:09:  8000000 
INFO  @ Mon, 16 May 2016 14:35:11:  9000000 
INFO  @ Mon, 16 May 2016 14:35:12:  10000000 
INFO  @ Mon, 16 May 2016 14:35:14:  11000000 
INFO  @ Mon, 16 May 2016 14:35:16:  12000000 
INFO  @ Mon, 16 May 2016 14:35:18:  13000000 
INFO  @ Mon, 16 May 2016 14:35:20:  14000000 
INFO  @ Mon, 16 May 2016 14:35:22:  15000000 
INFO  @ Mon, 16 May 2016 14:35:24:  16000000 
INFO  @ Mon, 16 May 2016 14:35:25:  17000000 
INFO  @ Mon, 16 May 2016 14:35:27:  18000000 
INFO  @ Mon, 16 May 2016 14:35:30:  19000000 
INFO  @ Mon, 16 May 2016 14:35:31:  20000000 
INFO  @ Mon, 16 May 2016 14:35:33:  21000000 
INFO  @ Mon, 16 May 2016 14:35:35:  22000000 
INFO  @ Mon, 16 May 2016 14:35:37:  23000000 
INFO  @ Mon, 16 May 2016 14:35:38:  24000000 
INFO  @ Mon, 16 May 2016 14:35:40:  25000000 
INFO  @ Mon, 16 May 2016 14:35:42:  26000000 
INFO  @ Mon, 16 May 2016 14:35:43:  27000000 
INFO  @ Mon, 16 May 2016 14:35:45:  28000000 
INFO  @ Mon, 16 May 2016 14:35:47:  29000000 
INFO  @ Mon, 16 May 2016 14:35:49:  30000000 
INFO  @ Mon, 16 May 2016 14:35:50:  31000000 
INFO  @ Mon, 16 May 2016 14:35:52:  32000000 
INFO  @ Mon, 16 May 2016 14:35:54:  33000000 
INFO  @ Mon, 16 May 2016 14:35:56:  34000000 
INFO  @ Mon, 16 May 2016 14:35:57:  35000000 
INFO  @ Mon, 16 May 2016 14:35:59:  36000000 
INFO  @ Mon, 16 May 2016 14:36:01:  37000000 
INFO  @ Mon, 16 May 2016 14:36:03:  38000000 
INFO  @ Mon, 16 May 2016 14:36:04:  39000000 
INFO  @ Mon, 16 May 2016 14:36:06:  40000000 
INFO  @ Mon, 16 May 2016 14:36:08:  41000000 
INFO  @ Mon, 16 May 2016 14:36:10:  42000000 
INFO  @ Mon, 16 May 2016 14:36:11:  43000000 
INFO  @ Mon, 16 May 2016 14:36:13:  44000000 
INFO  @ Mon, 16 May 2016 14:36:15:  45000000 
INFO  @ Mon, 16 May 2016 14:36:17:  46000000 
INFO  @ Mon, 16 May 2016 14:36:19:  47000000 
INFO  @ Mon, 16 May 2016 14:36:21:  48000000 
INFO  @ Mon, 16 May 2016 14:36:23:  49000000 
INFO  @ Mon, 16 May 2016 14:36:24:  50000000 
INFO  @ Mon, 16 May 2016 14:36:26:  51000000 
INFO  @ Mon, 16 May 2016 14:36:28:  52000000 
INFO  @ Mon, 16 May 2016 14:36:30:  53000000 
INFO  @ Mon, 16 May 2016 14:36:36: #1 tag size is determined as 51 bps 
INFO  @ Mon, 16 May 2016 14:36:36: #1 tag size = 51 
INFO  @ Mon, 16 May 2016 14:36:36: #1  total tags in treatment: 53816368 
INFO  @ Mon, 16 May 2016 14:36:36: #1 finished! 
INFO  @ Mon, 16 May 2016 14:36:36: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 14:36:36: #2 Skipped... 
INFO  @ Mon, 16 May 2016 14:36:36: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 14:36:36: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 14:36:36: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 14:36:36: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 14:36:36: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 14:36:36: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 14:39:08: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 14:39:08: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 14:39:08: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 14:39:08: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 14:39:08: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 14:46:10: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 14:46:12: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 14:46:14: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_summits.bed 
INFO  @ Mon, 16 May 2016 14:46:15: Done! 
INFO  @ Mon, 16 May 2016 14:46:19: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 14:48:15: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 14:49:07: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 14:49:56: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 14:55:49: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 14:59:20: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 15:11:31: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 15:13:20: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 15:14:09: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 15:15:01: Values in your input bedGraph files will be multiplied by 53.816368 ... 
INFO  @ Mon, 16 May 2016 15:21:48: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 15:22:43: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 15:26:06: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_ppois.bdg'!

Num	26
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31
Name	filt_top_peaks rep1
Thread	thread_Root
PID	119619

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 15:36:02
End	2016-05-16 15:36:18
Elapsed	00:00:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	27
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_32
Name	filt_top_peaks rep1
Thread	thread_Root
PID	119621

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 15:36:02
End	2016-05-16 15:36:13
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	28
ID	task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33
Name	filt_top_peaks rep2
Thread	thread_Root
PID	119623

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 15:36:02
End	2016-05-16 15:36:14
Elapsed	00:00:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	29
ID	task.callpeak_etc.filt_top_peaks_rep2.line_25.id_34
Name	filt_top_peaks rep2
Thread	thread_Root
PID	119631

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 15:36:02
End	2016-05-16 15:36:12
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	30
ID	task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35
Name	filt_top_peaks pooled
Thread	thread_Root
PID	119639

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 15:36:02
End	2016-05-16 15:36:14
Elapsed	00:00:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	31
ID	task.callpeak_etc.filt_top_peaks_pooled.line_25.id_36
Name	filt_top_peaks pooled
Thread	thread_Root
PID	119653

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-16 15:36:02
End	2016-05-16 15:36:11
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	32
ID	task.idr.idr2_rep1_rep2.line_61.id_37
Name	idr2 rep1-rep2
Thread	thread_Root
PID	119979

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus	1
Mem

Start	2016-05-16 15:36:19
End	2016-05-16 15:36:19
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.png /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Dependencies

 
# SYS command. line 63

 if [[ -f $(which activate) ]]; then source activate bds_atac_py3; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 65

 idr --samples /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/pooled_rep/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt --rank p.value --soft-idr-threshold 0.1 \
			--plot --use-best-multisummit-IDR

# SYS command. line 69

 idr_thresh_transformed=$(awk -v p=0.1 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 72

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz

# SYS command. line 75

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz

# SYS command. line 78

 bedtools intersect -v -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz; bedtools intersect -v -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz

# SYS command. line 80

 gzip -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt

    
--------------------Stderr--------------------
Error: could not find environment: bds_atac_py3

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2:/software/modulefiles/bedtools/2.23.0:/software/modulefiles/rsem/1.2.21
string	_ZSH_TMUX_FIXED_CONFIG	/users/pangwei/.oh-my-zsh/plugins/tmux/tmux.extra.conf
bool	allowEmpty	false
string[]	args	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC9/ATAC9-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC9/ATAC9-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC10/ATAC10-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC10/ATAC10-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
string	C_INCLUDE_PATH	/software/samtools/samtools-1.2/include/htslib
bool	canFail	false
int	cpus	1
int	cpusLocal	48
int	day	86400
real	E	2.718281828459045
int	G	1073741824
string	HOME	/users/pangwei/
int	hour	3600
int	K	1024
string	LANG	en_US.UTF-8
string	LC_CTYPE	en_US.UTF-8
string	LD_LIBRARY_PATH	/software/samtools/samtools-1.2/lib:/usr/local/cudnn-3/lib64/:/usr/local/cudnn-3/lib64/
string	LESS	-R
string	LOADEDMODULES	modsappsdir/modsappsdir:samtools/1.2:bedtools/2.23.0:rsem/1.2.21
string	LOGNAME	pangwei
string	LSCOLORS	Gxfxcxdxbxegedabagacad
int	M	1048576
string	MAIL	/var/mail/pangwei
string	MANPATH	/software/samtools/samtools-1.2/share/man:/usr/share/man
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESAPPSDIR	/software
string	MODULESHOME	/software/env_module/3.2.10
string	node
string	OLDPWD	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4
int	P	1125899906842624
string	PAGER	less
string	PATH	/software/RSEM/rsem-1.2.21/:/software/bedtools/2.23.0/bin:/software/samtools/samtools-1.2/bin:/users/pangwei/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
real	PI	3.141592653589793
string	ppwd	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string	programName	atac.bds
string	programPath	/users/pangwei/bds_atac/atac.bds
string	PWD	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string	PYTHONPATH	/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:
string	queue
int	retry	0
string	SAMTOOLS_HOME	/software/samtools/samtools-1.2/bin
string	SHELL	/usr/bin/zsh
string	SHLVL	2
string	SSH_AUTH_SOCK	/tmp/ssh-5gr8qSU2WF/agent.74700
string	SSH_CLIENT	171.65.76.244 36245 22
string	SSH_CONNECTION	171.65.76.244 49273 171.65.76.236 22
string	SSH_TTY	/dev/pts/0
string	system	local
int	T	1099511627776
string	TERM	screen
string	THEANO_FLAGS	device=gpu6,floatX=float32,warn_float64=warn,optimizer_excluding=cudnn
int	timeout	-1
string	TMUX	/tmp/tmux-1077/default,106699,3
string	TMUX_PANE	%3
string	USER	pangwei
string	UTIL_SCRIPTS_DIR	/users/pangwei/av_scripts
int	walltimeout	8640000
int	week	604800
string	WWW	/srv/www/kundaje/pangwei
string	XDG_RUNTIME_DIR	/run/user/1077
string	XDG_SESSION_ID	1907
string	ZSH	/users/pangwei//.oh-my-zsh
string	ZSH_TMUX_TERM	screen

BigDataScript report: atac.bds

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